Strain identifier

BacDive ID: 11660

Type strain: Yes

Species: Paenibacillus sediminis

Strain Designation: GT-H3, GTH-3

Strain history: CIP <- 2013, DSMZ <- S.T. Lee, Inst. of Science and Technol. Yuseong-gu, Daejon, Republic of Korea: strain GTH-3

NCBI tax ID(s): 664909 (species)

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General

@ref: 17237

BacDive-ID: 11660

DSM-Number: 23491

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, rod-shaped

description: Paenibacillus sediminis GT-H3 is an aerobe, spore-forming, mesophilic bacterium that was isolated from tidal flat.

NCBI tax id

  • NCBI tax id: 664909
  • Matching level: species

strain history

@refhistory
17237<- S. T. Lee, KAIST; GTH-3
122536CIP <- 2013, DSMZ <- S.T. Lee, Inst. of Science and Technol. Yuseong-gu, Daejon, Republic of Korea: strain GTH-3

doi: 10.13145/bacdive11660.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Paenibacillaceae
  • genus: Paenibacillus
  • species: Paenibacillus sediminis
  • full scientific name: Paenibacillus sediminis Wang et al. 2012

@ref: 17237

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus sediminis

full scientific name: Paenibacillus sediminis Wang et al. 2012

strain designation: GT-H3, GTH-3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30269positive6 µm0.5 µmrod-shapedno
69480yes92.676
69480positive100
122536negativerod-shapedno

pigmentation

  • @ref: 30269
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17237R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830; with strain-specific modifications) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l MnSO4 0.01 g/l Distilled water
122536CIP Medium 372yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=372

culture temp

@refgrowthtypetemperaturerange
17237positivegrowth30mesophilic
30269positivegrowth04-55

culture pH

  • @ref: 30269
  • ability: positive
  • type: growth
  • pH: 6.5-8.5
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 30269
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30269yes
69481yes100
69480yes100

halophily

  • @ref: 30269
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3026917234glucose+carbon source
3026917306maltose+carbon source

enzymes

@refvalueactivityec
30269catalase+1.11.1.6
30269cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
17237tidal flatWest Sea, adjacent to Ganghwa Island (37°42' 02'' N 126° 22' 38'' E),Republic of KoreaKORAsia37.7006126.377
122536Tidal flatWest seaRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Tidal flat

taxonmaps

  • @ref: 69479
  • File name: preview.99_72877.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_31019;97_39236;98_51046;99_72877&stattab=map
  • Last taxonomy: Paenibacillus sediminis subclade
  • 16S sequence: GQ355277
  • Sequence Identity:
  • Total samples: 989
  • soil counts: 649
  • aquatic counts: 124
  • animal counts: 58
  • plant counts: 158

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
172371Risk group (German classification)
1225361Risk group (French classification)

Sequence information

16S sequences

  • @ref: 17237
  • description: Paenibacillus sediminis strain GTH-3 16S ribosomal RNA gene, partial sequence
  • accession: GQ355277
  • length: 1452
  • database: ena
  • NCBI tax ID: 664909

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus sediminis DSM 23491GCA_017873765contigncbi664909
66792Paenibacillus sediminis strain DSM 23491664909.3wgspatric664909
66792Paenibacillus sediminis DSM 234912913409695draftimg664909

GC content

@refGC-contentmethod
1723745.9high performance liquid chromatography (HPLC)
3026945.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes89.268yes
anaerobicno96.412yes
halophileno87.879no
spore-formingyes95.809yes
glucose-utilyes88.312yes
thermophileno64.005no
flagellatedyes53.08yes
motileyes78.526yes
aerobicyes91.2yes
glucose-fermentno90.511no

External links

@ref: 17237

culture collection no.: DSM 23491, CIP 110613, LMG 25635

straininfo link

  • @ref: 80884
  • straininfo: 405459

literature

  • topic: Phylogeny
  • Pubmed-ID: 21784963
  • title: Paenibacillus sediminis sp. nov., a xylanolytic bacterium isolated from a tidal flat.
  • authors: Wang L, Baek SH, Cui Y, Lee HG, Lee ST
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.032102-0
  • year: 2011
  • mesh: DNA, Bacterial/genetics, Geologic Sediments/*microbiology, Molecular Sequence Data, Paenibacillus/*classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Xylans/*metabolism
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17237Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23491)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23491
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
30269Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2661028776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
80884Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID405459.1StrainInfo: A central database for resolving microbial strain identifiers
122536Curators of the CIPCollection of Institut Pasteur (CIP 110613)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110613